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fix: shrinkwrap setting incorrect lockfileVersion

Fix: #3962

When created from a hidden lockfile, shrinkwrap was always setting the
lockfileVersion to 3. The shrinkwrap command also needed to be updated
to log the correct message based on the lockfileVersion config instead
of the static lockfileVersion.

With these fixes, it was possible to log a better message whenever we
are changing the lockfileVersion, either from a config or any existing
lockfile.

Lastly, the tests for shrinkwrap were completely refactored to use the
real npm and test all conceivable scenarios, as well as removing usage
of `util.promisify` in favor of `fs.promises` now that we've dropped
support for Node 10.

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